Hinny research adds to knowledge of horse and donkey genomes

The genetics of the female hinny, born from the mating of a horse stallion and a jenny donkey, were analyzed using a process called trio-binning.
An aged hinny, pictured in the US. ©  Sage Ross/Ragesoss, CC BY-SA 4.0 via Wikimedia Commons

Researchers have improved our understanding of both the horse and donkey X chromosome in a study of the genetic make-up of a hinny.

The genetics of the female hinny, born from the mating of a horse stallion and a jenny donkey, were analyzed using a process called trio-binning.

Trio-binning uses short reads from two parental genomes to partition long reads from their offspring into haplotype-specific bins, followed by independent assembly of each haplotype.

The technique has been successfully applied to mammalian hybrids to obtain high-quality haploid assemblies of the two parent species.

Matthew Jevit and his fellow researchers, writing in the journal Scientific Reports, said the sequence assembly of the X chromosome in most animal reference genomes lags those of the other chromosomes (the autosomes), despite its biomedical importance and evolutionary interest.

The main challenge of studying the X chromosome, they said, is its structural complexity.

Currently, the most frequently used approach for research and clinical sequencing is the highly accurate and relatively inexpensive short-read Illumina technology. However, it has limited ability to assemble the most structurally complex parts of the genome.

The study team’s aim in using the trio-binning approach was to improve the assemblies of the horse and donkey X chromosomes and learn more about functional elements.

The authors said the single haplotype assemblies generated from the hinny significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes.

They added over 15 megabytes of missing sequence to both X chromosomes, 60 megabytes to donkey autosomes and corrected many errors in the donkey and some in the horse reference genomes.

Other findings helped to advance knowledge of the boundaries, size and location of several elements, as well as identifying distinct differences in the horse and donkey pseudoautosomal boundaries.

Despite this progress, the mapping of the two X chromosomes is still not complete, the study team said.

The authors said an important outcome of the study was identifying the horse and donkey pseudoautosomal boundaries and demarcating the pseudoautosomal regions at sequence level.

In addition to the haploid assemblies of the horse and donkey X chromosomes, the trio-binning approach also produced haploid assemblies for all horse and donkey autosomes.

The new haploid assemblies in the study improved the horse and donkey autosomes, whereas the improvements for donkey chromosomes were extensive compared to the current chromosome-level reference EquAsi134.

Despite this, many complex sequences remain unassigned in both species, they said.

“In conclusion, the improvements that were made for the horse and donkey X chromosomes are expected to advance the study of X-linked conditions, X chromosome regulation, meiotic behavior of the sex chromosomes, and sex chromosome evolution in equids.

“Likewise, the important additional products of this study — the more accurate, more complete, and contiguous assemblies of horse and donkey autosomes, contribute to molecular studies of equid biology and evolution.”

The study team comprised Jevit, Caitlin Castaneda, Brian Davis and Terje Raudsepp, all with Texas A&M University; Nandina Paria, with Texas Scottish Rite Hospital for Children in Dallas, Texas; Pranab Das, with the ICAR-National Research Centre on Pig in India; Donald Miller and Douglas Antczak, with Cornell University in New York State; and Theodore Kalbfleisch, with the Maxwell H. Gluck Equine Research Center, part of the University of Kentucky.

Jevit, M.J., Castaneda, C., Paria, N. et al. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 13, 20180 (2023). https://doi.org/10.1038/s41598-023-47583-x

The study, published under a Creative Commons License, can be read here

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